Whole-genome resequencing reveals genetic indels of feathered-leg traits in domestic chickens

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dc.contributor.authorYang, Shaohuaen_US
dc.contributor.authorShi, Zhaoyuanen_US
dc.contributor.authorOu, Iaoqianen_US
dc.contributor.authorLiu, Guoqingen_US
dc.date.accessioned2020-11-18T10:20:50Z
dc.date.available2020-11-18T10:20:50Z
dc.date.issued2019-05
dc.description.abstractWhole-genome resequencing provides the opportunity to explore the genomic variations and pave way for further functional assays to map the economical trait loci. In this study, we sequenced the genomes of mixed chicken samples from a full-sib family, with feathered and unfeathered legs at an average effective depth of 4.43×, using Illumina Hiseq 2000 instruments. Over 2.1 million nonredundant short indels (1–71 bp) were obtained. Among them, 16,375 common indels that were polymorphic between the comparison groups were revealed for further analysis. The majority of the common differential indels (76.52%) were novel. Follow-up validation assays confirmed that 80% randomly selected indels represented true variations. The indels were annotated based on the chicken genome sequence assembly. As a result, 16,375 indels were found to be located within 2756 annotated genes, with only 33 (0.202%) located in exons. By integrated analysis of the 2756 genes with gene function and known quantitative trait loci, we identified a total of 24 promising candidate genes potentially affecting feathered-leg trait, i.e. FGF1, FGF4, FGF10, FGFR1, FRZB, WNT1, WNT3A, WNT11, PCDH1, PCDH10, PCDH19, SOX3, BMP2, NOTCH2, TGF-β2, DLX5, REPS2, SCN3B, TCF20, FGF3, FSTL1, WNT7B, ELOVL2 and FGF8. Our findings provide a basis for further study and reveal key genes for feathered-leg trait in chickens.en_US
dc.identifier.affiliationsCollege of Food Science and Bioengineering, Hefei University of Technology, 193 Tunxi Road, Hefei 230009, Anhui, People’s Republic of Chinaen_US
dc.identifier.citationYang Shaohua, Shi Zhaoyuan, Ou Iaoqian, Liu Guoqing. Whole-genome resequencing reveals genetic indels of feathered-leg traits in domestic chickens. Journal of Genetics. 2019 May; 98: 1-8en_US
dc.identifier.issn0022-1333
dc.identifier.issn0973-7731
dc.identifier.placeIndiaen_US
dc.identifier.urihttps://imsear.searo.who.int/handle/123456789/215449
dc.languageenen_US
dc.publisherIndian Academy of Sciencesen_US
dc.relation.volume98en_US
dc.source.urihttps://www.ias.ac.in/article/fulltext/jgen/098/0047en_US
dc.subjectwhole-genome resequencingen_US
dc.subjectindelsen_US
dc.subjectfeathered-leg traiten_US
dc.subjectchicken.en_US
dc.titleWhole-genome resequencing reveals genetic indels of feathered-leg traits in domestic chickensen_US
dc.typeJournal Articleen_US
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